Knot localization in proteins.

The backbones of proteins form linear chains. In the case of some proteins, these chains can be characterized as forming linear open knots. The knot type of the full chain reveals only limited information about the entanglement of the chain since, for example, subchains of an unknotted protein can form knots and subchains of a knotted protein can form different types of knots than the entire protein. To understand fully the entanglement within the backbone of a given protein, a complete analysis of the knotting within all of the subchains of that protein is necessary. In the present article, we review efforts to characterize the full knotting complexity within individual proteins and present a matrix that conveys information about various aspects of protein knotting. For a given protein, this matrix identifies the precise localization of knotted regions and shows the knot types formed by all subchains. The pattern in the matrix can be considered as a knotting fingerprint of that protein. We observe that knotting fingerprints of distantly related knotted proteins are strongly conserved during evolution and discuss how some characteristic motifs in the knotting fingerprints are related to the structure of the knotted regions and their possible biological role.

The role of the right parietal cortex in sound localization: a chronometric single pulse transcranial magnetic stimulation study.

Auditory spatial functions, including the ability to discriminate between the positions of nearby sound sources, are subserved by a large temporo-parieto-frontal network. With the aim of determining whether and when the parietal contribution is critical for auditory spatial discrimination, we applied single pulse transcranial magnetic stimulation on the right parietal cortex 20, 80, 90 and 150 ms post-stimulus onset while participants completed a two-alternative forced choice auditory spatial discrimination task in the left or right hemispace. Our results reveal that transient TMS disruption of right parietal activity impairs spatial discrimination when applied at 20 ms post-stimulus onset for sounds presented in the left (controlateral) hemispace and at 80 ms for sounds presented in the right hemispace. We interpret our finding in terms of a critical role for controlateral temporo-parietal cortices over initial stages of the building-up of auditory spatial representation and for a right hemispheric specialization in integrating the whole auditory space over subsequent, higher-order processing stages.

Ventricular arrhythmia in coronary artery disease: limits of a risk stratification strategy based on the ejection fraction alone and impact of infarct localization.

AIMS: Estimates of the left ventricular ejection fraction (LVEF) in patients with life-threatening ventricular arrhythmias related to coronary artery disease (CAD) have rarely been reported despite it has become the basis for determining patient's eligibility for prophylactic defibrillator. We aimed to determine the extent and distribution of reduced LVEF in patients with sustained ventricular tachycardia or ventricular fibrillation. METHODS AND RESULTS: 252 patients admitted for ventricular arrhythmia related to CAD were included: 149 had acute myocardial infarction (MI) (Group I, 59%), 54 had significant chronic obstructive CAD suggestive of an ischaemic arrhythmic trigger (Group II, 21%) and 49 patients had an old MI without residual ischaemia (Group III, 19%). 34% of the patients with scar-related arrhythmias had an LVEF > or =40%. Based on pre-event LVEF evaluation, it can be estimated that less than one quarter of the whole study population had a known chronic MI with severely reduced LVEF. In Group III, the proportion of inferior MI was significantly higher than anterior MI (81 vs. 19%; absolute difference, -62; 95% confidence interval, -45 to -79; P < or = 0.0001), though median LVEF was higher in inferior MI (0.37 +/- 10 vs. 0.29 +/- 10; P = 0.0499). CONCLUSION: Patients included in defibrillator trials represent only a minority of the patients at risk of sudden cardiac death. By applying the current risk stratification strategy based on LVEF, more than one third of the patients with old MI would not have qualified for a prophylactic defibrillator. Our study also suggests that inferior scars may be more prone to ventricular arrhythmia compared to anterior scars.

Differential subcellular localization of phosphorylated neurofilament and tau proteins in degenerating neurons of the human entorhinal cortex.

A panel of novel monoclonal antibodies was tested on the human entorhinal cortex for the recognition of age- and disease-related changes of neurofilament proteins (NF). Several antibodies identified phosphorylated NF-H subunit, which occurred preferentially in those aged between 60 and 80 years and were localized in degenerating neurons. Such neurons also contained neurofibrillary tangles, but neurofilament aggregates did not co-localize with tangles, nor did the quantity nor the number of NF-positive neurons correlate with the severity of Alzheimer's disease. This points to a susceptibility of NF in a subset of neurons for phosphorylation- and metabolically related morphological changes during neurodegeneration.

Cell-specific localization of monocarboxylate transporters, MCT1 and MCT2, in the adult mouse brain revealed by double immunohistochemical labeling and confocal microscopy.

Recent evidence suggests that lactate could be a preferential energy substrate transferred from astrocytes to neurons. This would imply the presence of specific transporters for lactate on both cell types. We have investigated the immunohistochemical localization of two monocarboxylate transporters, MCT1 and MCT2, in the adult mouse brain. Using specific antibodies raised against MCT1 and MCT2, we found strong immunoreactivity for each transporter in glia limitans, ependymocytes and several microvessel-like elements. In addition, small processes distributed throughout the cerebral parenchyma were immunolabeled for monocarboxylate transporters. Double immunofluorescent labeling and confocal microscopy examination of these small processes revealed no co-localization between glial fibrillary acidic protein and monocarboxylate transporters, although many glial fibrillary acidic protein-positive processes were often in close apposition to elements labeled for monocarboxylate transporters. In contrast, several elements expressing the S100beta protein, another astrocytic marker found to be located in distinct parts of the same cell when compared with glial fibrillary acidic protein, were also strongly immunoreactive for MCT1, suggesting expression of this transporter by astrocytes. In contrast, MCT2 was expressed in a small subset of microtubule-associated protein-2-positive elements, indicating a neuronal localization. In conclusion, these observations are consistent with the possibility that lactate, produced and released by astrocytes (via MCT1), could be taken up (via MCT2) and used by neurons as an energy substrate.

The spatio-temporal brain dynamics of processing and integrating sound localization cues in humans.

Interaural intensity and time differences (IID and ITD) are two binaural auditory cues for localizing sounds in space. This study investigated the spatio-temporal brain mechanisms for processing and integrating IID and ITD cues in humans. Auditory-evoked potentials were recorded, while subjects passively listened to noise bursts lateralized with IID, ITD or both cues simultaneously, as well as a more frequent centrally presented noise. In a separate psychophysical experiment, subjects actively discriminated lateralized from centrally presented stimuli. IID and ITD cues elicited different electric field topographies starting at approximately 75 ms post-stimulus onset, indicative of the engagement of distinct cortical networks. By contrast, no performance differences were observed between IID and ITD cues during the psychophysical experiment. Subjects did, however, respond significantly faster and more accurately when both cues were presented simultaneously. This performance facilitation exceeded predictions from probability summation, suggestive of interactions in neural processing of IID and ITD cues. Supra-additive neural response interactions as well as topographic modulations were indeed observed approximately 200 ms post-stimulus for the comparison of responses to the simultaneous presentation of both cues with the mean of those to separate IID and ITD cues. Source estimations revealed differential processing of IID and ITD cues initially within superior temporal cortices and also at later stages within temporo-parietal and inferior frontal cortices. Differences were principally in terms of hemispheric lateralization. The collective psychophysical and electrophysiological results support the hypothesis that IID and ITD cues are processed by distinct, but interacting, cortical networks that can in turn facilitate auditory localization.

Distinct subcellular localization of beta-tubulin epitopes in the adult mouse brain.

A panel of monoclonal antibodies specific of alpha-tubulin (TU-01, TU-09) and beta-tubulin (TU-06, TU-13) subunits was used to study the location of N-terminal structural domains of tubulin in adult mouse brain. The specificity of antibodies was confirmed b immunoblotting experiments. Immunohistochemical staining of vibratome sections from cerebral cortex, cerebellum, hippocampus, and corpus callosum showed that antibodies TU-01, TU-09, and TU-13 reacted with neuronal and glial cells and their processes, whereas the TU-06 antibody stained only the perikarya. Dendrites and axons were either unstained or their staining was very weak. As the TU-06 epitope is located on the N-terminal structural domain of beta-tubulin, the observed staining pattern cannot be interpreted as evidence of a distinct subcellular localization of beta-tubulin isotypes or known post-translational modifications. The limited distribution of the epitope could, rather, reflect differences between the conformations of tubulin molecules in microtubules of somata and neurites or, alternatively, a specific masking of the corresponding region on the N-terminal domain of beta-tubulin by interacting protein(s) in dendrites and axons.

Site-specific conjugation of a radioiodinated phenethylamine derivative to a monoclonal antibody results in increased radioactivity localization in tumor.

The preparation of a novel radioiodination reagent, the (aminooxy)acetyl derivative of (p-[125]-iodophenyl)ethylamine, is described. Conventional radioiodination of proteins involves the formation of iodotyrosine residues, but for in vivo applications such as thyroid or stomach immunoscintigraphy, the susceptibility of these residues to tissue dehalogenases constitutes a serious disadvantage. Using our new compound, which has a particularly nonreactive aromatic ring, we confirm and extend studies published by other workers indicating the much greater in vivo stability of iodophenyl compounds compared to the more conventional iodophenolic ones. In addition, the aminooxy group of our reagent gives a stable and specific linkage to aldehyde groups formed by periodate oxidation on the sugar moiety of antibody molecules. In vitro, favorable binding activity and high stability was obtained with a (([125I]iodoaryl)amino)oxy labeled monoclonal antibody directed against carcinoembryonic antigen. In vivo, using paired labeling experiments in nude mice bearing colon carcinoma xenografts, the (([125I]iodoaryl)amino)oxy-MAb (MAb = monoclonal antibody) was compared with the same MAb 131I-labeled by conventional chloramine-T method. Tumor 125I concentration of (arylamino)oxy MAb (measured as percent injected dose per gram) was significantly higher as compared to values obtained with a conventionally labeled 131I antibody. Additionally, thyroid uptake, an indicator of iodine release from the antibody, was up to 25 times lower after injection of 125I-MAb obtained by the new method as compared to the conventionally iodinated 131I-MAb.

Using the Number of Pores on Fingerprint Images to Detect Spoofing Attacks

Abstract-Due to the growing use of biometric technologies inour modern society, spoofing attacks are becoming a seriousconcern. Many solutions have been proposed to detect the use offake "fingerprints" on an acquisition device. In this paper, wepropose to take advantage of intrinsic features of friction ridgeskin: pores. The aim of this study is to investigate the potential ofusing pores to detect spoofing attacks.Results show that the use of pores is a promising approach. Fourmajor observations were made: First, results confirmed that thereproduction of pores on fake "fingerprints" is possible. Second,the distribution of the total number of pores between fake andgenuine fingerprints cannot be discriminated. Third, thedifference in pore quantities between a query image and areference image (genuine or fake) can be used as a discriminatingfactor in a linear discriminant analysis. In our sample, theobserved error rates were as follows: 45.5% of false positive (thefake passed the test) and 3.8% of false negative (a genuine printhas been rejected). Finally, the performance is improved byusing the difference of pore quantity obtained between adistorted query fingerprint and a non-distorted referencefingerprint. By using this approach, the error rates improved to21.2% of false acceptation rate and 8.3% of false rejection rate.

Interpretation of partial fingermarks using an automated fingerprint identification system

Abstract : In the subject of fingerprints, the rise of computers tools made it possible to create powerful automated search algorithms. These algorithms allow, inter alia, to compare a fingermark to a fingerprint database and therefore to establish a link between the mark and a known source. With the growth of the capacities of these systems and of data storage, as well as increasing collaboration between police services on the international level, the size of these databases increases. The current challenge for the field of fingerprint identification consists of the growth of these databases, which makes it possible to find impressions that are very similar but coming from distinct fingers. However and simultaneously, this data and these systems allow a description of the variability between different impressions from a same finger and between impressions from different fingers. This statistical description of the withinand between-finger variabilities computed on the basis of minutiae and their relative positions can then be utilized in a statistical approach to interpretation. The computation of a likelihood ratio, employing simultaneously the comparison between the mark and the print of the case, the within-variability of the suspects' finger and the between-variability of the mark with respect to a database, can then be based on representative data. Thus, these data allow an evaluation which may be more detailed than that obtained by the application of rules established long before the advent of these large databases or by the specialists experience. The goal of the present thesis is to evaluate likelihood ratios, computed based on the scores of an automated fingerprint identification system when the source of the tested and compared marks is known. These ratios must support the hypothesis which it is known to be true. Moreover, they should support this hypothesis more and more strongly with the addition of information in the form of additional minutiae. For the modeling of within- and between-variability, the necessary data were defined, and acquired for one finger of a first donor, and two fingers of a second donor. The database used for between-variability includes approximately 600000 inked prints. The minimal number of observations necessary for a robust estimation was determined for the two distributions used. Factors which influence these distributions were also analyzed: the number of minutiae included in the configuration and the configuration as such for both distributions, as well as the finger number and the general pattern for between-variability, and the orientation of the minutiae for within-variability. In the present study, the only factor for which no influence has been shown is the orientation of minutiae The results show that the likelihood ratios resulting from the use of the scores of an AFIS can be used for evaluation. Relatively low rates of likelihood ratios supporting the hypothesis known to be false have been obtained. The maximum rate of likelihood ratios supporting the hypothesis that the two impressions were left by the same finger when the impressions came from different fingers obtained is of 5.2 %, for a configuration of 6 minutiae. When a 7th then an 8th minutia are added, this rate lowers to 3.2 %, then to 0.8 %. In parallel, for these same configurations, the likelihood ratios obtained are on average of the order of 100,1000, and 10000 for 6,7 and 8 minutiae when the two impressions come from the same finger. These likelihood ratios can therefore be an important aid for decision making. Both positive evolutions linked to the addition of minutiae (a drop in the rates of likelihood ratios which can lead to an erroneous decision and an increase in the value of the likelihood ratio) were observed in a systematic way within the framework of the study. Approximations based on 3 scores for within-variability and on 10 scores for between-variability were found, and showed satisfactory results. Résumé : Dans le domaine des empreintes digitales, l'essor des outils informatisés a permis de créer de puissants algorithmes de recherche automatique. Ces algorithmes permettent, entre autres, de comparer une trace à une banque de données d'empreintes digitales de source connue. Ainsi, le lien entre la trace et l'une de ces sources peut être établi. Avec la croissance des capacités de ces systèmes, des potentiels de stockage de données, ainsi qu'avec une collaboration accrue au niveau international entre les services de police, la taille des banques de données augmente. Le défi actuel pour le domaine de l'identification par empreintes digitales consiste en la croissance de ces banques de données, qui peut permettre de trouver des impressions très similaires mais provenant de doigts distincts. Toutefois et simultanément, ces données et ces systèmes permettent une description des variabilités entre différentes appositions d'un même doigt, et entre les appositions de différents doigts, basées sur des larges quantités de données. Cette description statistique de l'intra- et de l'intervariabilité calculée à partir des minuties et de leurs positions relatives va s'insérer dans une approche d'interprétation probabiliste. Le calcul d'un rapport de vraisemblance, qui fait intervenir simultanément la comparaison entre la trace et l'empreinte du cas, ainsi que l'intravariabilité du doigt du suspect et l'intervariabilité de la trace par rapport à une banque de données, peut alors se baser sur des jeux de données représentatifs. Ainsi, ces données permettent d'aboutir à une évaluation beaucoup plus fine que celle obtenue par l'application de règles établies bien avant l'avènement de ces grandes banques ou par la seule expérience du spécialiste. L'objectif de la présente thèse est d'évaluer des rapports de vraisemblance calcul és à partir des scores d'un système automatique lorsqu'on connaît la source des traces testées et comparées. Ces rapports doivent soutenir l'hypothèse dont il est connu qu'elle est vraie. De plus, ils devraient soutenir de plus en plus fortement cette hypothèse avec l'ajout d'information sous la forme de minuties additionnelles. Pour la modélisation de l'intra- et l'intervariabilité, les données nécessaires ont été définies, et acquises pour un doigt d'un premier donneur, et deux doigts d'un second donneur. La banque de données utilisée pour l'intervariabilité inclut environ 600000 empreintes encrées. Le nombre minimal d'observations nécessaire pour une estimation robuste a été déterminé pour les deux distributions utilisées. Des facteurs qui influencent ces distributions ont, par la suite, été analysés: le nombre de minuties inclus dans la configuration et la configuration en tant que telle pour les deux distributions, ainsi que le numéro du doigt et le dessin général pour l'intervariabilité, et la orientation des minuties pour l'intravariabilité. Parmi tous ces facteurs, l'orientation des minuties est le seul dont une influence n'a pas été démontrée dans la présente étude. Les résultats montrent que les rapports de vraisemblance issus de l'utilisation des scores de l'AFIS peuvent être utilisés à des fins évaluatifs. Des taux de rapports de vraisemblance relativement bas soutiennent l'hypothèse que l'on sait fausse. Le taux maximal de rapports de vraisemblance soutenant l'hypothèse que les deux impressions aient été laissées par le même doigt alors qu'en réalité les impressions viennent de doigts différents obtenu est de 5.2%, pour une configuration de 6 minuties. Lorsqu'une 7ème puis une 8ème minutie sont ajoutées, ce taux baisse d'abord à 3.2%, puis à 0.8%. Parallèlement, pour ces mêmes configurations, les rapports de vraisemblance sont en moyenne de l'ordre de 100, 1000, et 10000 pour 6, 7 et 8 minuties lorsque les deux impressions proviennent du même doigt. Ces rapports de vraisemblance peuvent donc apporter un soutien important à la prise de décision. Les deux évolutions positives liées à l'ajout de minuties (baisse des taux qui peuvent amener à une décision erronée et augmentation de la valeur du rapport de vraisemblance) ont été observées de façon systématique dans le cadre de l'étude. Des approximations basées sur 3 scores pour l'intravariabilité et sur 10 scores pour l'intervariabilité ont été trouvées, et ont montré des résultats satisfaisants.

Angiotensinergic innervation of the kidney: Localization and relationship with catecholaminergic postganglionic and sensory nerve fibers.

We describe an angiotensin (Ang) II-containing innervation of the kidney. Cryosections of rat, pig and human kidneys were investigated for the presence of Ang II-containing nerve fibers using a mouse monoclonal antibody against Ang II (4B3). Co-staining was performed with antibodies against synaptophysin, tyrosine 3-hydroxylase, and dopamine beta-hydroxylase to detect catecholaminergic efferent fibers and against calcitonin gene-related peptide to detect sensory fibers. Tagged secondary antibodies and confocal light or laser scanning microscopy were used for immunofluorescence detection. Ang II-containing nerve fibers were densely present in the renal pelvis, the subepithelial layer of the urothelium, the arterial nervous plexus, and the peritubular interstitium of the cortex and outer medulla. They were infrequent in central veins and the renal capsule and absent within glomeruli and the renal papilla. Ang II-positive fibers represented phenotypic subgroups of catecholaminergic postganglionic or sensory fibers with different morphology and intrarenal distribution compared to their Ang II-negative counterparts. The Ang II-positive postganglionic fibers were thicker, produced typically fusiform varicosities and preferentially innervated the outer medulla and periglomerular arterioles. Ang II-negative sensory fibers were highly varicose, prevailing in the pelvis and scarce in the renal periphery compared to the rarely varicose Ang II-positive fibers. Neurons within renal microganglia displayed angiotensinergic, cate-cholaminergic, or combined phenotypes. Our results suggest that autonomic fibers may be an independent source of intrarenal Ang II acting as a neuropeptide co-transmitter or neuromodulator. The angiotensinergic renal innervation may play a distinct role in the neuronal control of renal sodium reabsorption, vasomotion and renin secretion.

Role of the sub-cellular localization of RasGAP fragment N2 for its ability to sensitize cancer cells to genotoxin-induced apoptosis.

The specific sensitization of tumor cells to the apoptotic response induced by genotoxins is a promising way of increasing the efficacy of chemotherapies. The RasGAP-derived fragment N2, while not regulating apoptosis in normal cells, potently sensitizes tumor cells to cisplatin- and other genotoxin-induced cell death. Here we show that fragment N2 in living cells is mainly located in the cytoplasm and only minimally associated with specific organelles. The cytoplasmic localization of fragment N2 was required for its cisplatin-sensitization property because targeting it to the mitochondria or the ER abrogated its ability to increase the death of tumor cells in response to cisplatin. These results indicate that fragment N2 requires a spatially constrained cellular location to exert its anti-cancer activity.

Localization of breakage points in knotted strings

It is a common macroscopic observation that knotted ropes or fishing lines under tension easily break at the knot. However, a more precise localization of the breakage point in knotted macroscopic strings is a difficult task. In the present work, the tightening of knots was numerically simulated, a comparison of strength of different knots was experimentally performed and a high velocity camera was used to precisely localize the site where knotted macroscopic strings break. In the case of knotted spaghetti, the breakage occurs at the position with high curvature at the entry to the knot. This localization results from joint contributions of loading, bending and friction forces into the complex process of knot breakage. The present simulations and experiments are in agreement with recent molecular dynamics simulations of a knotted polymer chain and with experiments performed on actin and DNA filaments. The strength of the knotted string is greatly reduced (down to 50%) by the presence of a knot, therefore reducing the resistance to tension of all materials containing chains of any sort. The present work with macroscopic strings revels some important aspects, which are not accessible by experiments with microscopic chains.